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Hughes was born to privilege as the grandson of Charles Evans Hughes, 1916Republican Party nominee for President, and claimed in his memoirs to have been used as a "campaign baby" as an infant. Hughes' father left for World War I while Stuart was still an infant, returning a year later when his son was three. Stuart was his parents' second child and second son and was born only 14 months after his elder brother, Charles Evans Hughes, III; the couple was later to have two daughters as well.

Hughes then attended graduate school at Harvard University, where he wrote his thesis on "The Crisis of the Imperial French Economy, 1810-1812." He was in Paris working on this thesis when World War II started on September 1, 1939. Hughes soon returned to Cambridge.

Hughes, by then a lieutenant colonel, was honorably discharged from active duty in 1946 and was soon reassigned as a civilian intelligence analyst, returning to Europe. In this role, he was to befriend pioneering blackState Department official Ralph Bunche. In the State Department, Hughes bemoaned the rise of the Cold War mentality. In late 1947, he left to return to Harvard as an instructor and as the associate director of its new Russian Research Center. However, Hughes felt that he unwittingly sabotaged his career there by his early support for former Vice PresidentHenry Wallace for President in 1948. In 1950, Hughes married his first wife, Suzanne, a member of a wealthy and influential FrenchProtestant family. Failing to be published as a historian at a level sufficient to allow him to be promoted in the atmosphere of the Harvard of that time, and somewhat ostracized for his activism, Hughes left Harvard for Stanford University in 1952 at the height of the McCarthy era.

While in California, Hughes was published at a level sufficient to encourage Harvard to recall him, which it did in 1957. During this second stay at Harvard, Hughes became involved with SANE (then the Committee for a Sane Nuclear Policy, now Peace Action). Early in this period, he also engaged in a series of debates with a young Harvard professor of government, Henry Kissinger. In 1962, Hughes filed as an independent candidate for the final two years of the unexpired U.S. Senate term of President John F. Kennedy. Major-party candidates included Democratic Party members Edward M. Kennedy, the President's youngest brother, and Eddie McCormack, nephew of the Speaker of the House, and RepublicanGeorge C. Lodge. Hughes collected well over the 72,000 signatures then required under Massachusetts law to be placed on the ballot as an independent candidate; the September Democratic primary eliminated McCormick from further contention.

For most of the campaign, Hughes was taken seriously, even engaging in two televised debates with Lodge. (Kennedy, by now an overwhelming favorite, declined to participate.) Any chance, however slim, that Hughes might have had to win the election or even receive widespread support was destroyed in the aftermath of the Cuban Missile Crisis, only weeks before the election, in which the President and his other brother, Bobby, took the nation "to the brink" of nuclear confrontation with the Soviet Union. A pro-nuclear disarmament candidate suddenly seemed unrealistic and out of touch; Hughes received less than two per cent of the vote and far fewer votes than he previously had signatures. ("Ted" Kennedy won the election resoundingly and served in the seat until his death in 2009.)

As a beneficiary of it, Hughes saw the value of psychoanalysis. His widow, Judith Hughes, is a European historian and psychoanalyst. He, in the words of his wife, “could not have lived the life he did, at least the last 40-plus years of it, without benefit of psychoanalysis.” [2]

As a historian Stuart Hughes saw enormous value of the Freudian world view applied to history. In Gentleman Rebel he reported being close to his Harvard colleague Erik Erikson and serving in the ”supporting cast” of psychohistory.[3] When Richard Schoenwald established the first psychohistory newsletter (the predecessor to The Psychohistory Review), Hughes made serious contributuions and encouraged the new and bold direction of the publication.

An important bibliographer of psychohistory, William Gilmore, calls “History and Psychoanalysis: The Explanation of Motive,” in Hughes’ book, History as Art and as Science (1964), an indispensable “classic” and “a must reading.”[4] Hughes’ memoirs are particularly revealing, as he does not begin his account with any mention of his distinguished family, but instead with a question from his psychoanalyst, Avery Weisman.

Early in 1963, Hughes and Suzanne filed for divorce. In the fall of 1963, Hughes agreed to become co-chairman of the SANE organization, alongside renowned pediatrician and fellow activist Dr. Benjamin Spock. In March 1964, Hughes married his second wife, Judy, whom he initially had met as one of his graduate school students. As SANE expanded its anti-nuclear activities to include anti-Vietnam War activism, Hughes was branded by the State Department's Passport Office as a potential subversive. He also found himself in an increasingly isolated position on the Harvard faculty, opposed to both the Vietnam War and also many of the actions that began to be taken in opposition to it. Hughes, however, served as the sole chairman of SANE from 1967 to 1970 after Spock resigned his co-chairmanship.

Hughes also became associated with male support for feminism. In part, this seems to have been prompted by his perception of academic discrimination against his wife after she had earned her own doctorate. It was this discrimination that, in large measure, seems to have led to the Hughes' departure from Harvard for the University of California at San Diego; unlike his first departure from Harvard, it could not now be linked to any failure to have been sufficiently published. They moved to San Diego in 1975; Hughes taught at UCSD until taking emeritus status in 1989 and died in the suburb of La Jolla (actual site of the UCSD campus), following a protracted illness, in 1999.